6AAE

Crystal structure of Chloramphenicol-Metabolizaing Enzyme EstDL136


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of chloramphenicol-metabolizing enzyme EstDL136 from a metagenome.

Kim, S.H.Kang, P.A.Han, K.T.Lee, S.W.Rhee, S.K.

(2019) PLoS One 14: e0210298-e0210298

  • DOI: 10.1371/journal.pone.0210298
  • Primary Citation of Related Structures:  
    6AAE, 6IEY

  • PubMed Abstract: 
  • Metagenomes often convey novel biological activities and therefore have gained considerable attention for use in biotechnological applications. Recently, metagenome-derived EstDL136 was found to possess chloramphenicol (Cm)-metabolizing features. Sequence analysis showed EstDL136 to be a member of the hormone-sensitive lipase (HSL) family with an Asp-His-Ser catalytic triad and a notable substrate specificity ...

    Metagenomes often convey novel biological activities and therefore have gained considerable attention for use in biotechnological applications. Recently, metagenome-derived EstDL136 was found to possess chloramphenicol (Cm)-metabolizing features. Sequence analysis showed EstDL136 to be a member of the hormone-sensitive lipase (HSL) family with an Asp-His-Ser catalytic triad and a notable substrate specificity. In this study, we determined the crystal structures of EstDL136 and in a complex with Cm. Consistent with the high sequence similarity, the structure of EstDL136 is homologous to that of the HSL family. The active site of EstDL136 is a relatively shallow pocket that could accommodate Cm as a substrate as opposed to the long acyl chain substrates typical of the HSL family. Mutational analyses further suggested that several residues in the vicinity of the active site play roles in the Cm-binding of EstDL136. These results provide structural and functional insights into a metagenome-derived EstDL136.


    Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EsteraseA, B317uncultured bacteriumMutation(s): 0 
Gene Names: estDL136
EC: 3.1.1.1
UniProt
Find proteins for G3CR02 (uncultured bacterium)
Explore G3CR02 
Go to UniProtKB:  G3CR02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3CR02
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B],
J [auth B],
C [auth A],
D [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.943α = 90
b = 153.586β = 90
c = 44.243γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Rural Development AdministrationKorea, Republic OfPJ01325801
National Research Foundation (Korea)Korea, Republic Of2017R1A2B4002860
Rural Development AdministrationKorea, Republic OfPJ 0109390

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release